Let me see if I can help…
In the full report, please scroll to section 4.3.1. In the last diagram of that section we offer this view that you are referring to where we have grouped all the PD3D versions, all the XP11 versions and stacked them against FS2020.
To answer your question about this diagram: “we have considered all positive use responses (from “Infrequently” to “Most of the time”) for each simulator version by each respondent, and grouped them into the same graph.”
About your question on how we grouped the answering alternatives: Well, that depends on which analysis you are doing. One simulator might offer free upgrade to the next version, like you mention for X-Plane, but that might not true for other simulators. Also, the various versions of simulators do have different feature sets and are in varying degrees of maturity so… not sure what to tell you there - we did it in these both ways so that there at least are these two ways of looking at the data.
Remember, if you want it sliced any other way we have put up the dataset for you to download and you can juggle it inExcel in any way you want. 
Am I helping at all, or just adding to the confusion?
Edit: Typo